From 30806f18d1e65fecf06597310282eb90eeb95f98 Mon Sep 17 00:00:00 2001
From: linglp <linglp@umich.edu>
Date: Tue, 30 Jul 2024 16:20:13 -0400
Subject: [PATCH] add sequence diagram for create_manifests

---
 .github/workflows/pdoc.yml      |  1 +
 schematic/manifest/generator.py | 68 ++++++++++++++++++++++-----------
 2 files changed, 47 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/pdoc.yml b/.github/workflows/pdoc.yml
index 187b5adb1..7ffd73bbb 100644
--- a/.github/workflows/pdoc.yml
+++ b/.github/workflows/pdoc.yml
@@ -5,6 +5,7 @@ on:
   push:
     branches:
       - develop
+      - develop-add-mermaid
   workflow_dispatch:  # Allow manually triggering the workflow
 
 # security: restrict permissions for CI jobs.
diff --git a/schematic/manifest/generator.py b/schematic/manifest/generator.py
index d7eb16c30..1664c48ee 100644
--- a/schematic/manifest/generator.py
+++ b/schematic/manifest/generator.py
@@ -1,38 +1,38 @@
-from collections import OrderedDict
 import json
 import logging
-import networkx as nx
-from openpyxl.styles import Font, Alignment, PatternFill
-from openpyxl import load_workbook
-from openpyxl.utils.dataframe import dataframe_to_rows
 import os
-import pandas as pd
+from collections import OrderedDict
 from pathlib import Path
-import pygsheets as ps
 from tempfile import NamedTemporaryFile
-from typing import Any, Dict, List, Optional, Tuple, Union, BinaryIO, Literal
+from typing import Any, BinaryIO, Dict, List, Literal, Optional, Tuple, Union
+
+import networkx as nx
+import pandas as pd
+import pygsheets as ps
+from openpyxl import load_workbook
+from openpyxl.styles import Alignment, Font, PatternFill
+from openpyxl.utils.dataframe import dataframe_to_rows
+from opentelemetry import trace
 
+from schematic.configuration.configuration import CONFIG
 from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer
-from schematic.schemas.data_model_parser import DataModelParser
 from schematic.schemas.data_model_json_schema import DataModelJSONSchema
+from schematic.schemas.data_model_parser import DataModelParser
 
+# TODO: This module should only be aware of the store interface
+# we shouldn't need to expose Synapse functionality explicitly
+from schematic.store.synapse import SynapseStorage
+from schematic.utils.df_utils import load_df, update_df
 from schematic.utils.google_api_utils import (
-    execute_google_api_requests,
     build_service_account_creds,
+    execute_google_api_requests,
+    export_manifest_drive_service,
+)
+from schematic.utils.schema_utils import (
+    DisplayLabelType,
+    extract_component_validation_rules,
 )
-from schematic.utils.df_utils import update_df, load_df
-from schematic.utils.schema_utils import extract_component_validation_rules
 from schematic.utils.validate_utils import rule_in_rule_list
-from schematic.utils.schema_utils import DisplayLabelType
-
-# TODO: This module should only be aware of the store interface
-# we shouldn't need to expose Synapse functionality explicitly
-from schematic.store.synapse import SynapseStorage
-
-from schematic.configuration.configuration import CONFIG
-from schematic.utils.google_api_utils import export_manifest_drive_service
-
-from opentelemetry import trace
 
 logger = logging.getLogger(__name__)
 tracer = trace.get_tracer("Schematic")
@@ -1657,6 +1657,30 @@ def create_manifests(
 
         Returns:
             Union[List[str], List[pd.DataFrame]]: a list of Googlesheet URLs, a list of pandas dataframes or excel file paths
+
+        ::: mermaid
+        sequenceDiagram
+        participant User
+        participant Function
+        participant DataModelParser
+        participant DataModelGraph
+        participant ManifestGenerator
+        User->>Function: call create_manifests
+        Function->>Function: check dataset_ids and validate inputs
+        Function->>DataModelParser: parse data model
+        DataModelParser-->>Function: return parsed data model
+        Function->>DataModelGraph: generate graph
+        DataModelGraph-->>Function: return graph data model
+        alt data_types == "all manifests"
+            Function->>ManifestGenerator: create manifests for all components
+        else
+            loop for each data_type
+                Function->>ManifestGenerator: create single manifest
+            end
+        end
+        ManifestGenerator-->>Function: return results
+        Function-->>User: return manifests based on output_format
+        :::
         """
         if dataset_ids:
             # Check that the number of submitted data_types matches